5clo

Crystal structure of a 4-oxalocrotonate tautomerase mutant in complex with nitrostyrene at 2.3 Angstrom

Method: X-RAY DIFFRACTION Dmax: 108.6 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

2-hydroxymuconate tautomerase

Pseudomonas putida

UniProt Q01468

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–60 Chain B; UniProt 2–60 Chain C; UniProt 2–60 Chain D; UniProt 2–60 Chain E; UniProt 2–60 Chain F; UniProt 2–60 Fragment:UNP residues 2-60 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;0.1 M PCTP buffer, 25% PEG 1500, 5 mM nitrostyrene, 5 % (v/v) DMSO Resolution 2.30 Å R-free 0.276
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 2–60 Chain H; UniProt 2–60 Chain I; UniProt 2–60 Chain J; UniProt 2–60 Chain K; UniProt 2–60 Chain L; UniProt 2–60 Fragment:UNP residues 2-60 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;0.1 M PCTP buffer, 25% PEG 1500, 5 mM nitrostyrene, 5 % (v/v) DMSO Resolution 2.30 Å R-free 0.276
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain M; UniProt 2–60 Chain N; UniProt 2–60 Chain O; UniProt 2–60 Chain P; UniProt 2–60 Chain Q; UniProt 2–60 Chain R; UniProt 2–60 Fragment:UNP residues 2-60 Mutation:M45Y, F50A NS8 trans beta nitrostyrene × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;0.1 M PCTP buffer, 25% PEG 1500, 5 mM nitrostyrene, 5 % (v/v) DMSO Resolution 2.30 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 4OT1_PSEPU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–59; UniProt 2–60 Author chain B; PDBConstruct 1–59; UniProt 2–60 Author chain C; PDBConstruct 1–59; UniProt 2–60 Author chain D; PDBConstruct 1–59; UniProt 2–60 Author chain E; PDBConstruct 1–59; UniProt 2–60 Author chain F; PDBConstruct 1–59; UniProt 2–60 Author chain G; PDBConstruct 1–59; UniProt 2–60 Author chain H; PDBConstruct 1–59; UniProt 2–60 Author chain I; PDBConstruct 1–59; UniProt 2–60 Author chain J; PDBConstruct 1–59; UniProt 2–60 Author chain K; PDBConstruct 1–59; UniProt 2–60 Author chain L; PDBConstruct 1–59; UniProt 2–60 Author chain M; PDBConstruct 1–59; UniProt 2–60 Author chain N; PDBConstruct 1–59; UniProt 2–60 Author chain O; PDBConstruct 1–59; UniProt 2–60 Author chain P; PDBConstruct 1–59; UniProt 2–60 Author chain Q; PDBConstruct 1–59; UniProt 2–60 Author chain R; PDBConstruct 1–59; UniProt 2–60

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5clo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5clo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5clo
Deposition date deposition_date2015-07-16
Structure title titleCrystal structure of a 4-oxalocrotonate tautomerase mutant in complex with nitrostyrene at 2.3 Angstrom
Keywords keywords4-Oxalocrotonate tautomerase, beta-alpha-beta structural motif, tautomerase superfamily, isomerase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.18
Radius of gyration Rg (electron density) rg_electron33.35
Forward intensity I(0) i0192666000.00
Molecular weight molecular_weight110230.0 kDa
Excluded volume excluded_volume138130 ų
Envelope volume envelope_volume176860 ų
Hydration-shell volume shell_volume44238 ų
Envelope diameter envelope_diameter107.9
Shell Rg shell_rg39.94
Envelope Rg envelope_rg32.84
Shape Rg shape_rg33.34
Total Rg total_rg33.88
Total atoms total_atoms7763
Residues n_residues1025
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.6
Rg (real space) rg_real34.11
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real1.9270e+08
I(0) uncertainty (real space) i0_real_error3.1420e+06
Rg (reciprocal space) rg_reciprocal34.15
I(0) (reciprocal space) i0_reciprocal192700000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.616
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40910000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.938

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd5cloa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clob_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clod_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloe_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clof_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clog_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clok_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clol_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clom_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clon_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloo_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clop_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5cloq_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd5clor_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like

CATH v4.4 (18 domains)

Domain ID domain_id5cloA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloM00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloN00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloO00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloP00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloQ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id5cloR00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor

8. Citations (1)

9. Files and Curves (10)